Genetic Diversity and Population Structure in Chinese Indigenous Poplar (Populus simonii) Populations Using Microsatellite Markers

Wei, Zunzheng; Du, Qingzhang; Zhang, Jinfeng; Li, Bai-Lian; Zhang, Deqiang

doi:10.1007/s11105-012-0527-2

Cited by 46 publications

(30 citation statements)

References 53 publications

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“…This agrees with the results obtained for other Salicaceae species, such as S. viminalis (92.3%)28, Salix caprea (91.7%)30, Populus simonii (85.8%)52, P. euphratica (85.5%) and P. pruinosa (78.8%)53 based on SSR markers. This result may have been obtained because Salicaceae species are generally dioecious and combine anemophilous and entomophilous pollination with an outcrossing breeding system and high dispersal ability, which could enhance intraspecific diversity and reduce population differentiation275455.…”

Section: Discussionsupporting

confidence: 90%

De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila

Jia

Yang

Sun

et al. 2016

Sci Rep

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Salix psammophila, a sandy shrub known as desert willow, is regarded as a potential biomass feedstock and plays an important role in maintaining local ecosystems. However, a lack of genomic data and efficient molecular markers limit the study of its population evolution and genetic breeding. In this study, chromosome counts, flow cytometry and SSR analyses indicated that S. psammophila is tetraploid. A total of 6,346 EST-SSRs were detected based on 71,458 de novo assembled unigenes from transcriptome data. Twenty-seven EST-SSR markers were developed to evaluate the genetic diversity and population structure of S. psammophila from eight natural populations in Northern China. High levels of genetic diversity (mean 10.63 alleles per locus; mean HE 0.689) were dectected in S. psammophila. The weak population structure and little genetic differentiation (pairwise FST = 0.006–0.016) were found among Population 1-Population 7 (Pop1-Pop7; Inner Mongolia and Shaanxi), but Pop8 (Ningxia) was clearly separated from Pop1-Pop7 and moderate differentiation (pairwise FST = 0.045–0.055) was detected between them, which may be influenced by local habitat conditions. Molecular variance analyses indicated that most of the genetic variation (94.27%) existed within populations. These results provide valuable genetic informations for natural resource conservation and breeding programme optimisation of S. psammophila.

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Section: Discussionsupporting

confidence: 90%

De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila

Jia

Yang

Sun

et al. 2016

Sci Rep

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“…Coupled with ΔK parameter computation [16], the percentage of admixture of each individual obtained for K = 3 [17] was used in the subsequent association analyses (Table S2 in Additional file 1). Relative kinship estimates based on the 20 SSR loci showed that 63.0% of the pair-wise kinship estimates equal to 0 suggests that almost two-thirds of the total pairs of accessions showed no relationship.…”

Section: Resultsmentioning

confidence: 99%

Association mapping for morphological and physiological traits in Populus simonii

Wei

Zhang

et al. 2014

BMC Genet

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BackgroundTo optimize marker-assisted selection programs, knowledge of the genetic architecture of phenotypic traits is very important for breeders. Generally, most phenotypes, e.g. morphological and physiological traits, are quantitatively inherited, and thus detection of the genes underlying variation for these traits is difficult. Association mapping based on linkage disequilibrium has recently become a powerful approach to map genes or quantitative trait loci (QTL) in plants.ResultsIn this study, association analysis using 20 simple sequence repeat (SSR) markers was performed to detect the marker loci linked to 13 morphological traits and 10 physiological traits in a wild P. simonii population that consisted of 528 individuals sampled from 16 sites along the Yellow River in China. Based on a model controlling for both population structure (Q) and relative kinship (K), three SSR markers (GCPM_616-1 in 31.2 Mb on LG I, GCPM_4055-2 in 5.7 Mb on LG XV, and GCPM_3142 of unknown location) were identified for seven traits. GCPM_616-1 was associated with five morphological traits (R2 = 5.14-10.09%), whereas GCPM_3142 (15.03%) and GCPM_4055-2 (13.26%) were associated with one morphological trait and one physiological trait, respectively.ConclusionsThe results suggest that this wild population is suitable for association mapping and the identified markers will be suitable for marker-assisted selection breeding or detection of target genes or QTL in the near future.

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“…1). Each individual was randomly selected and separated at least 100 m from the next one to avoid clonal structure due to root suckers to the largest possible extent (Wei et al, 2013;Čortan et al, 2016). All selected individuals have been evaluated as the one of good vitality (grade 1 and 2).…”

Section: Genetic Analysismentioning

confidence: 99%

Viability and genetic diversity of Populus nigra population from riparian forest in SNR Gornje Podunavlje

Čortan¹,

Tubić²

2017

Dendrobiology

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Populus nigra L. is one of the rarest and most endangered tree species in Western and Central Europe. Its genetic diversity is of great importance in enabling a native riparian population to survive and reproduce under changing environmental conditions. The aim of this research was assessment of P. nigra viability in one of the best preserved riparian ecosystems in Europe, Special Nature Reserve "Gornje Podunavlje" (Upper Danube), Serbia. Additionally, the analysis of the genetic diversity was made to support the effective conservation in the future. During our study, we have mapped 931 P. nigra trees, which were used for the assessment of present native population. Furthermore, we used 14 microsatellite markers to assess the genetic structure of this this population. Viability assessment showed considerable occurrence of P. nigra in the research area, even though the results show fragmentation. P. nigra occurs mostly individually or in small groups of trees, and has a non-sustainable age structure due to insufficient or lacking regeneration. Despite the limited size of the studied population, the apparent overall genetic diversity was high (He = 0.759) and comparable to other known native populations of P. nigra along the Danube basin. However, the results also confirmed existence of recent bottleneck effect. Significantly positive and quite high F is value (0.147) was noted, which may be ascribed to the "Wahlund effect" because of the population substructure that was revealed by the STRUC-TURE analysis (K=2). Although results say that coverage of native stands is not so promising, most of selected trees within our research assessed showed good viability with potential for natural reproduction However, the problem is that suitable areas for natural seedling establishment are scarce and with that gene flow is probably limited. The fragmentation of the area must be reduced and isolated stands must be interlinked as there is need to create larger non-fragmented areas.

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Genetic Diversity and Population Structure in Chinese Indigenous Poplar (Populus simonii) Populations Using Microsatellite Markers

Cited by 46 publications

References 53 publications

De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila

De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila

Association mapping for morphological and physiological traits in Populus simonii

Viability and genetic diversity of Populus nigra population from riparian forest in SNR Gornje Podunavlje

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